5NYH

Crystal Structure of Hsp90-alpha N-Domain in complex with Indazole derivative

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors.

Schuetz, D.A., Richter, L., Amaral, M., Grandits, M., Gradler, U., Musil, D., Buchstaller, H.P., Eggenweiler, H.M., Frech, M., Ecker, G.F.

(2018) J Med Chem 61: 4397-4411

  • DOI: 10.1021/acs.jmedchem.8b00080
  • Primary Citation of Related Structures:  
    5LO1, 5LO0, 5LNZ, 5LNY, 5OD7, 5OCI, 5ODX, 5NYH

  • PubMed Abstract: 

    • Residence time and more recently the association rate constant k on are increasingly acknowledged as important parameters for in vivo efficacy and safety of drugs. However, their broader consideration in drug development is limited by a lack of knowledge of how to optimize these parameters ...

    Residence time and more recently the association rate constant k on are increasingly acknowledged as important parameters for in vivo efficacy and safety of drugs. However, their broader consideration in drug development is limited by a lack of knowledge of how to optimize these parameters. In this study on a set of 176 heat shock protein 90 inhibitors, structure-kinetic relationships, X-ray crystallography, and molecular dynamics simulations were combined to retrieve a concrete scheme of how to rationally slow down on-rates. We discovered that an increased ligand desolvation barrier by introducing polar substituents resulted in a significant k on decrease. The slowdown was accomplished by introducing polar moieties to those parts of the ligand that point toward a hydrophobic cavity. We validated this scheme by increasing polarity of three Hsp90 inhibitors and observed a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation in residence time. This prolongation was driven by transition state destabilization rather than ground state stabilization.

    Organizational Affiliation: 

    Department of Pharmaceutical Chemistry , University of Vienna , UZA 2, Althanstrasse 14 , 1090 Vienna , Austria.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alphaA229Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
GTEx:  ENSG00000080824
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9EK (Subject of Investigation/LOI)
Query on 9EK
Download Ideal Coordinates CCD File 
 B [auth A]~{N}-methyl-~{N}-(4-morpholin-4-ylphenyl)-6-oxidanyl-3-pyrrolidin-1-ylcarbonyl-2~{H}-indazole-5-carboxamide
C24 H27 N5 O4
PAGPOZMFSDBEOC-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9EK Binding MOAD:  5NYH Kd: 18.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.979α = 90
b = 88.54β = 90
c = 97.091γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  


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Entry History 

Deposition Data

  • Deposited Date: 2017-05-11 
  • Released Date: 2018-04-18 
    • Deposition Author(s): Amaral, M.

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2018-06-06
    Changes: Data collection, Database references